Hi Will,

We did manage to solve that problem by changing the Apache
configuration. We added "AllowEncodedSlashes On" to httpd.conf. I'm not
sure why the URL encoding changed, only that it did. See if that helps you.

Best,

Scott

On Tue, May 10, 2016 at 8:17 PM, Will Holtz <who...@lygos.com> wrote:

> Hi Scott,
>
> I've recently hit the exact same problem. Have you had any success since
> then with resolving this? I did some poking around and made a bit of
> progress, but still no solution.
>
> The Data Manager page under Run Data Manager Tools contains URLs like this:
>
>
> https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1
>
> Loading that URL results in an attempted load of:
>
>
> https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1/build
> ?
>
> Which results in a 404 error. I believe the escaping of the slashes is
> accidental, as the they are in the path and not in parameters. Changing the
> %2F to / as shown here:
>
>
> https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1/build
> ?
>
> results in the URL being found and you get back a bunch of JSON about the
> tool. I tried looking in the Galaxy code to see if I could quickly
> determine where the /root controller is, but I wasn't successful. Perhaps
> this is now enough information that one of the developers might be able to
> help us.
>
> -Will
>
> On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi <scott.b.szakony...@nd.edu
> > wrote:
>
>> Hello,
>>
>> I'm having an odd problem after updating to the latest version of Galaxy.
>> My users prepare data for analysis using data manager tools, such as
>> "data_manager_bwa_mem_index_builder". When an attempt is made to run one of
>> these tools, a pop up window opens stating "Tool request failed" and
>> underneath "Uncaught error". I've pored over all the Galaxy system logs and
>> can't find anything that might indicate what is happening. I've uninstalled
>> and reinstalled the data manager tools, restarted both the Galaxy service
>> and the server, to no avail. I get this same error with any installed data
>> manager, yet all the standard tools are executing correctly and don't seem
>> to be having any issues.
>>
>> If anyone can offer some insight or suggestions for resolving this issue,
>> I'd be most appreciative.
>>
>> Best regards,
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>>
>> ___________________________________________________________
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>
>
>
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-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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